ArticleProceedings of the National Academy of Sciences of the United States of America2009
A force field for virtual atom molecular mechanics of proteins.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Choosing the right density for a concentrated protein system like gluten in a coarse-grained model.European biophysics journal : EBJ · 2023Article
- Viscoelastic properties of wheat gluten in a molecular dynamics study.PLoS computational biology · 2021Article
- Sixty-five years of the long march in protein secondary structure prediction: the final stretch?Briefings in bioinformatics · 2018Article
- Intrinsic Localized Modes in Proteins.Scientific reports · 2015Article
- ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability.Nucleic acids research · 2015Article
- New Insights into Protein (Un)Folding Dynamics.The journal of physical chemistry letters · 2015Article
- An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials.Journal of chemical theory and computation · 2014Article
- Recent advances in transferable coarse-grained modeling of proteins.Advances in protein chemistry and structural biology · 2014Review
- Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains.Journal of chemical theory and computation · 2012Article
- A generic force field for protein coarse-grained molecular dynamics simulation.International journal of molecular sciences · 2012Article
- Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Structural plasticity and conformational transitions of HIV envelope glycoprotein gp120.PloS one · 2012Article
- Normal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic models.Archives of biochemistry and biophysics · 2011Article
- Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Integrating ion mobility mass spectrometry with molecular modelling to determine the architecture of multiprotein complexes.PloS one · 2010Article
- Multiscale coarse-graining of the protein energy landscape.PLoS computational biology · 2010Article
- Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
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2 authors.
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Abstract
Activities of many biological macromolecules involve large conformational transitions for which crystallography can specify atomic details of alternative end states, but the course of transitions is often beyond the reach of computations based on full-atomic potential functions. We have developed a coarse-grained force field for molecular mechanics calculations based on the virtual interactions of C alpha atoms in protein molecules. This force field is parameterized based on the statistical distribution of the energy terms extracted from crystallographic data, and it is formulated to capture features dependent on secondary structure and on residue-specific contact information. The resulting force field is applied to energy minimization and normal mode analysis of several proteins. We find robust convergence in minimizations to low energies and energy gradients with low degrees of structural distortion, and atomic fluctuations calculated from the normal mode analyses correlate well with the experimental B-factors obtained from high-resolution crystal structures. These findings suggest that the virtual atom force field is a suitable tool for various molecular mechanics applications on large macromolecular systems undergoing large conformational changes.
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